Contacts of the helix formed by residues 6 - 15 (chain B) in PDB entry 1HXD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ASN* 3.2 21.5 - - - +
5B THR* 1.3 72.4 - - - +
7B PRO* 1.3 71.1 - - + +
9B LYS* 2.6 33.5 + - - +
10B LEU* 3.0 12.3 + - - +
29B LEU* 5.5 4.5 - - + +
31B MET* 4.1 17.3 - - + -
39B HIS* 3.6 36.3 - - + +
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Residues in contact with PRO 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASN* 2.9 22.4 - - + +
6B VAL* 1.3 93.0 - - + +
8B LEU* 1.3 58.9 + - - +
10B LEU* 2.7 29.1 - - + +
11B ILE* 2.7 15.8 + - - +
39B HIS* 3.7 15.5 - - + +
42B THR* 3.2 29.8 - - + -
43B LEU* 3.4 7.6 - - + +
46B TRP* 3.4 26.5 - - + -
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ASN* 3.0 23.3 - - - +
5B THR* 2.8 46.9 - - + +
7B PRO* 1.3 74.6 - - - +
9B LYS* 1.3 60.6 + - - +
11B ILE* 3.0 17.0 - - + +
12B ALA* 3.6 16.1 + - - +
46B TRP* 4.6 11.0 - - + -
85B PRO* 4.2 28.9 - - + -
86B VAL* 5.1 4.9 - - + -
127B PHE* 5.2 5.8 - - + -
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Residues in contact with LYS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B THR* 2.8 28.8 + - + +
6B VAL* 2.6 20.1 + - - +
8B LEU* 1.3 73.3 - - + +
10B LEU* 1.3 62.7 + - - +
12B ALA* 3.2 8.4 + - + +
13B LEU* 3.1 24.8 + - + +
28B THR 5.6 3.4 + - - -
29B LEU* 4.3 22.3 - - + +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL 3.0 8.8 + - - +
7B PRO* 2.7 39.5 - - + +
9B LYS* 1.3 75.4 - - - +
11B ILE* 1.3 72.9 + - - +
12B ALA 2.9 1.3 - - - -
13B LEU* 3.3 20.9 - - + -
14B LEU* 2.8 35.8 + - + +
25B LEU* 5.3 7.9 - - + -
29B LEU* 4.8 11.4 - - + -
36B ILE* 4.6 16.4 - - + +
39B HIS* 4.4 13.0 - - + -
40B ILE* 3.7 33.0 - - + -
43B LEU* 3.1 15.7 - - + -
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO 2.7 27.8 + - - +
8B LEU* 3.0 26.0 - - + +
10B LEU* 1.3 81.4 - - - +
12B ALA* 1.3 55.7 + - - +
14B LEU* 4.0 9.2 - - + -
15B ALA* 3.0 30.4 + - + +
43B LEU* 3.4 24.5 - - + -
48B VAL* 4.8 14.8 - - + -
50B VAL* 5.8 0.2 - - + -
60B LEU* 4.1 24.0 - - + -
64B ILE* 5.7 3.1 - - + -
66B LEU* 4.5 6.9 - - + +
127B PHE* 4.0 32.3 - - + -
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU 3.6 10.9 + - - +
9B LYS* 3.2 12.5 + - + +
10B LEU 2.9 0.6 - - - -
11B ILE* 1.3 85.5 - - - +
13B LEU* 1.3 63.2 + - + +
15B ALA* 3.8 9.5 + - - +
16B ASN 4.9 1.0 + - - -
66B LEU* 4.2 17.1 - - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS* 3.1 10.8 - - + +
10B LEU* 2.9 27.3 + - + +
12B ALA* 1.3 80.9 - - + +
14B LEU* 1.3 58.2 + - + +
16B ASN* 3.2 9.5 + - - +
20B HIS* 3.0 25.4 + - + +
25B LEU* 5.1 16.8 - - + -
28B THR* 4.5 14.4 - - + +
29B LEU* 3.5 28.3 - - + -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 2.8 33.3 + - + +
11B ILE* 4.0 10.3 - - + +
13B LEU* 1.3 76.3 - - + +
15B ALA* 1.4 51.3 + - - +
16B ASN* 2.9 18.9 + - - +
17B GLY* 2.9 15.9 + - - -
18B GLU 3.9 2.8 + - - +
20B HIS* 3.4 35.1 - - + +
25B LEU* 4.4 12.1 - - + -
40B ILE* 4.5 12.6 - - + -
43B LEU* 4.2 13.9 - - + -
50B VAL* 5.3 6.1 - - + -
58B TYR* 4.4 20.2 - - + +
59B SER* 4.7 3.4 - - - +
60B LEU* 3.6 24.2 - - + +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 3.0 20.7 + - + +
12B ALA 4.0 6.3 - - - +
13B LEU 3.5 1.6 - - - -
14B LEU* 1.4 70.5 - - - +
16B ASN* 1.3 55.3 + - - +
17B GLY 3.0 5.6 - - - -
60B LEU* 4.0 11.2 - - + +
63B PRO* 2.8 6.4 - - - +
64B ILE* 2.7 52.2 + - + +
66B LEU* 3.9 19.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il